Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily...
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oai:doaj.org-article:fb68d9af990646118b516f63dd5714ec2021-12-02T14:01:32ZCrystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli10.1038/s41598-020-79537-y2045-2322https://doaj.org/article/fb68d9af990646118b516f63dd5714ec2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79537-yhttps://doaj.org/toc/2045-2322Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily proteins are cleaved by their inherent AP lyase activities, other AP endonuclease activities or heat-promoted β-elimination. Although the HALFPIPE superfamily protein R.PabI, obtained from a hyperthermophilic archaea, Pyrococcus abyssi, shows weak AP lyase activity, HALFPIPE superfamily proteins in mesophiles, such as R.CcoLI from Campylobacter coli and R. HpyAXII from Helicobacter pylori, show significant AP lyase activities. To identify the structural basis for the AP lyase activity of R.CcoLI, we determined the structure of R.CcoLI by X-ray crystallography. The structure of R.CcoLI, obtained at 2.35-Å resolution, shows that a conserved lysine residue (Lys71), which is stabilized by a characteristic β-sheet structure of R.CcoLI, protrudes into the active site. The results of mutational assays indicate that Lys71 is important for the AP lyase activity of R.CcoLI. Our results help to elucidate the mechanism by which HALFPIPE superfamily proteins from mesophiles efficiently introduce double-strand breaks to specific sites on double-stranded DNA.Ken-ichi MiyazonoDelong WangTomoko ItoMasaru TanokuraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021) |
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Medicine R Science Q Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
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Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily proteins are cleaved by their inherent AP lyase activities, other AP endonuclease activities or heat-promoted β-elimination. Although the HALFPIPE superfamily protein R.PabI, obtained from a hyperthermophilic archaea, Pyrococcus abyssi, shows weak AP lyase activity, HALFPIPE superfamily proteins in mesophiles, such as R.CcoLI from Campylobacter coli and R. HpyAXII from Helicobacter pylori, show significant AP lyase activities. To identify the structural basis for the AP lyase activity of R.CcoLI, we determined the structure of R.CcoLI by X-ray crystallography. The structure of R.CcoLI, obtained at 2.35-Å resolution, shows that a conserved lysine residue (Lys71), which is stabilized by a characteristic β-sheet structure of R.CcoLI, protrudes into the active site. The results of mutational assays indicate that Lys71 is important for the AP lyase activity of R.CcoLI. Our results help to elucidate the mechanism by which HALFPIPE superfamily proteins from mesophiles efficiently introduce double-strand breaks to specific sites on double-stranded DNA. |
format |
article |
author |
Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura |
author_facet |
Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura |
author_sort |
Ken-ichi Miyazono |
title |
Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
title_short |
Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
title_full |
Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
title_fullStr |
Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
title_full_unstemmed |
Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli |
title_sort |
crystal structure and dna cleavage mechanism of the restriction dna glycosylase r.ccoli from campylobacter coli |
publisher |
Nature Portfolio |
publishDate |
2021 |
url |
https://doaj.org/article/fb68d9af990646118b516f63dd5714ec |
work_keys_str_mv |
AT kenichimiyazono crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT delongwang crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT tomokoito crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT masarutanokura crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli |
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